An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

Area of Science:

• Virology
• Immunology
• Structural Biology

Background:

• Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) utilizes its spike glycoprotein to bind the angiotensin-converting enzyme 2 (ACE2) receptor for host cell entry.
• Inhibiting the spike-ACE2 interaction is a key strategy for developing antiviral therapies against SARS-CoV-2.
• Alpaca-derived single domain antibodies (nanobodies) offer potential as therapeutic agents due to their small size and stability.

Purpose of the Study:

• To isolate and characterize a novel nanobody targeting the SARS-CoV-2 spike protein's receptor binding domain (RBD).
• To evaluate the efficacy of this nanobody in preventing ACE2 engagement and neutralizing SARS-CoV-2.
• To determine the structural basis of nanobody-RBD interaction for therapeutic development.

Main Methods:

• Isolation and characterization of alpaca single domain antibody fragment (Ty1).
• Binding affinity assays to measure Ty1's interaction with the SARS-CoV-2 RBD.
• Cryo-electron microscopy (cryo-EM) to determine the structure of the Ty1-RBD complex.
• Pseudovirus neutralization assays to assess antiviral activity.

Main Results:

• Ty1 specifically binds the SARS-CoV-2 RBD with high affinity, effectively blocking ACE2 interaction.
• Cryo-EM analysis revealed Ty1 binds an epitope accessible in both RBD conformations, sterically hindering ACE2 binding.
• Ty1, as a nanobody, neutralizes SARS-CoV-2 pseudovirus and can be produced at scale in bacteria.

Conclusions:

• Ty1 is a potent inhibitor of SARS-CoV-2 entry by directly targeting the spike RBD-ACE2 interface.
• The nanobody's high affinity, broad epitope accessibility, and potential for scalable manufacturing make it a promising candidate for COVID-19 intervention.
• Ty1 represents a viable therapeutic strategy against SARS-CoV-2 infection.